To interpret a coordinate (x, y, z), it is required that you know relative to
which origin the coordinates are expressed, you have to know the interpretation
of the three axes, and you have to know the units in which the numbers are
expressed. This information is sometimes called the coordinate system.

These letters help describe the coordinate system definition:

A/P means anterior/posterior

L/R means left/right

S/I means superior/inferior

For example: RAS means that the first dimension (X) points towards the right
hand side of the head, the second dimension (Y) points towards the Anterior
aspect of the head, and the third dimension (Z) points towards the top of the
head.

Besides coordinate systems, defined by their origin and direction of the axes,
BIDS defines "spaces" as an artificial frame of reference, created to describe
different anatomies in a unifying manner (see e.g.,
https://doi.org/10.1016/j.neuroimage.2012.01.024).
The "space" and all coordinates expressed in this space are by design a
transformation of the real world geometry, and nearly always different from the
individual subject space that it stems from. An example is the
Talairach-Tournoux space, which is constructed by piecewise linear scaling of an
individual's brain to that of the Talairach-Tournoux 1988 atlas. In the
Talairach-Tournoux space, the origin of the coordinate system is at the AC and
units are expressed in mm.

The coordinate systems below all relate to neuroscience and therefore to the
head or brain coordinates. Please be aware that all data acquisition starts with
"device coordinates" (scanner), which does not have to be identical to the
initial "file format coordinates" (DICOM), which are again different from the
"head" coordinates (e.g., NIFTI). Not only do device coordinate vary between
hardware manufacturers, but also the head coordinates differ, mostly due to
different conventions used in specific software packages developed by different
(commercial or academic) groups.

Generally, across the MEG, EEG, and iEEG modalities, the first two pieces of
information (origin, orientation) are specified in XXXCoordinateSystem, and
the units are specified in XXXCoordinateSystemUnits.

Allowed values for the XXXCoordinateSystem field come from a list of
restricted keywords, as listed in the sections below. If no value from the list
of restricted keywords fits, there is always the option to specify the value as
follows:

Other: Use this for other coordinate systems and specify further details
in the XXXCoordinateSystemDescription field

Restricted keywords for the XXXCoordinateSystem field in the
coordsystem.json file for iEEG datasets:

Pixels: If electrodes are localized in 2D space (only x and y are
specified and z is n/a), then the positions in this file must correspond to
the locations expressed in pixels on the photo/drawing/rendering of the
electrodes on the brain. In this case, coordinates must be (row,column)
pairs, with (0,0) corresponding to the upper left pixel and (N,0)
corresponding to the lower left pixel.

ACPC: The origin of the coordinate system is at the Anterior Commissure
and the negative y-axis is passing through the Posterior Commissure. The
positive z-axis is passing through a mid-hemispheric point in the superior
direction. The anatomical landmarks are determined in the individual's
anatomical scan and no scaling or deformations have been applied to the
individual's anatomical scan. For more information, see the
ACPC site on the FieldTrip
toolbox wiki.

The transformation of the real world geometry to an artificial frame of
reference is described in XXXCoordinateSystem.
Unless otherwise specified below, the origin is at the AC and the orientation of
the axes is RAS.
Unless specified explicitly in the sidecar file in the XXXCoordinateSystemUnits field,
the units are assumed to be mm.

Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" https://www.loni.usc.edu/research/atlases

ICBM452Warp5Space

Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" https://www.loni.usc.edu/research/atlases

IXI549Space

Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. http://www.brain-development.org/

fsaverage[3|4|5|6|sym]

DISCOURAGED, please use fsaverage without modifiers. Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template

fsaverage

The fsaverage is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of MNI305 space. The fsaverage atlas also defines a surface reference system (formerly described as fsaverage[3|4|5|6|sym]).

fsaverageSym

The fsaverage is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of MNI305 space. The fsaverageSym atlas also defines a symmetric surface reference system (formerly described as fsaveragesym).

fsLR

The fsLR is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to MNI152NLin6Asym. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image.

The following template identifiers are retained for backwards compatibility
of BIDS implementations.
Their use is NOT RECOMMENDED for new BIDS datasets and tooling, but their
presence MUST NOT produce a validation error.

The following template identifiers are RECOMMENDED for individual- and study-specific reference
spaces.
In order for these spaces to be interpretable, SpatialReference metadata MUST be provided, as
described in Common file level metadata fields.

In the case of multiple study templates, additional names may need to be defined.

Coordinate System

Description

individual

Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been refered to as fsnative.

study

Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined.

The scanner coordinate system is implicit and assumed by default if the derivative filename does not define anyspace-<label>.
Please note that space-scanner SHOULD NOT be used, it is mentioned in this specification to make its existence explicit.

Coordinate System

Description

scanner

The intrinsic coordinate system of the original image (the first entry of RawSources) after reconstruction and conversion to NIfTI or equivalent for the case of surfaces and dual volume/surface files.